GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruII-ABC in Pseudomonas fluorescens FW300-N2E3

Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate AO353_05475 AO353_05475 PTS fructose transporter subunit IIBC

Query= TCDB::P71012
         (635 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05475 AO353_05475 PTS
           fructose transporter subunit IIBC
          Length = 579

 Score =  441 bits (1135), Expect = e-128
 Identities = 234/519 (45%), Positives = 344/519 (66%), Gaps = 26/519 (5%)

Query: 122 TLLMREEIRKQLLEAESEDAI--IDIINQHDKDDDEEEEEEEAAPAPAGKGK----ILAV 175
           T+ M   + K++ ++    A+  +D + +   ++ +     +A   PA   K    ++AV
Sbjct: 66  TVDMSRFVGKRVFQSTPSQALQDVDAVLRRGAEEAQIYVAPQAVVEPATVSKTAPRLVAV 125

Query: 176 TACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQ 235
           TACPTG+AHTFMAA+AL++ AK LG +++VET GS G ++ L+AQ I DA  +++AAD +
Sbjct: 126 TACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAQAIADADVVLLAADIE 185

Query: 236 VEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAKGKSGS 295
           V  ERF GK++ +      +++ +  + KA+ +        G    AS+  +    K  +
Sbjct: 186 VATERFAGKKIYRCGTGIALKQAEATLNKALAE--------GKQETASSGVQGPAKKEKT 237

Query: 296 GIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDN 355
           G+    YKHL++GVS MLP VV GG+++A+SF +GI +    +P   T AAAL  IGGD 
Sbjct: 238 GV----YKHLLTGVSFMLPMVVAGGLMIALSFVFGITAF--KEPG--TLAAALMQIGGDT 289

Query: 356 ALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKV 415
           A KL+V +LAG+IA SIADRPG APGM+GG +A+   AGF+GG+IAGF+AGY    + + 
Sbjct: 290 AFKLMVPLLAGYIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFIAGYAAQAINR- 348

Query: 416 FTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMG 475
           +  +PQSL+ LKP+LI PL     TG++M +VV  PVA  +  LT++L+S+GT N +L+G
Sbjct: 349 YARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGLLESLTHFLDSMGTTNAILLG 408

Query: 476 IILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKF 535
           ++LGGMM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+G+ +AT I R KF
Sbjct: 409 VLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKF 468

Query: 536 TQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPH 595
            Q +REAG     +G  F++EGAIPFAA DPLRVIPA++ G A+AG L+ +F   L APH
Sbjct: 469 AQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGCKLMAPH 528

Query: 596 GGVFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKKP 631
           GG+FV  I    NH +LYLL+IV G+++ A++   VK+P
Sbjct: 529 GGLFVMLIPNAINHALLYLLAIVAGSLLTAVVYAAVKRP 567



 Score = 53.5 bits (127), Expect = 2e-11
 Identities = 30/103 (29%), Positives = 55/103 (53%), Gaps = 1/103 (0%)

Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230
           K+  VTACP G+  + + A  L   A+  G    VE + ++  + +L+A  +EDA  +++
Sbjct: 2   KLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEDAEWVLL 61

Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIY 273
            +   V+M RF GKRV Q   +  ++    ++ +   ++A IY
Sbjct: 62  VSTGTVDMSRFVGKRVFQSTPSQALQDVDAVLRRGA-EEAQIY 103


Lambda     K      H
   0.320    0.137    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 789
Number of extensions: 33
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 635
Length of database: 579
Length adjustment: 37
Effective length of query: 598
Effective length of database: 542
Effective search space:   324116
Effective search space used:   324116
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory